GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etoh-dh-nad in Marinobacter adhaerens HP15

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate GFF2063 HP15_2019 iron-containing alcohol dehydrogenase

Query= BRENDA::A4IP64
         (395 letters)



>lcl|FitnessBrowser__Marino:GFF2063 HP15_2019 iron-containing
           alcohol dehydrogenase
          Length = 385

 Score =  274 bits (700), Expect = 4e-78
 Identities = 162/376 (43%), Positives = 235/376 (62%), Gaps = 14/376 (3%)

Query: 17  GALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPLET 76
           G   +L   VK    K +L++TDP LVK GL+D  T+ L + G    ++  VV +PP+  
Sbjct: 17  GVTHRLGQIVKEHMGKKVLLVTDPGLVKAGLLDVATNSLNEAGVKYELFDGVVADPPVSV 76

Query: 77  GEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGLPK 136
            E A+A AR+   D VIG GGGS++D+AKL A+L   +  + D   + G    + K LP 
Sbjct: 77  VEAALADAREAGVDGVIGFGGGSSMDVAKLIALLIGGEEKLDD---VYGVGQAKGKRLPL 133

Query: 137 ILIPTTSGTGSEVTNISVLSL-ETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAATGID 195
           I IPTT+GTGSEVT IS++++ ET K  V    LL D+A++D +LT+ +P  VTAATGID
Sbjct: 134 IQIPTTAGTGSEVTPISIITVGETEKKGVVAPQLLPDIALLDAELTLGLPAHVTAATGID 193

Query: 196 ALTHAVEAYVSVNAS--PTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAGL 253
           A+ HA+E+Y S +A+  P S  LA  A+RL+  ++  AV +GS+ +AR DM  G+ LAG 
Sbjct: 194 AMVHAIESYTSASANNNPVSKALAREALRLLGANIETAVKDGSNVKARSDMLLGAMLAGQ 253

Query: 254 AFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMA----DIFNALG 309
           AF N+ VA VHALAYP+GG FH+ HG SNA++LP+VM +  + C +  +    D+F  L 
Sbjct: 254 AFANSPVAAVHALAYPIGGIFHVPHGLSNALVLPHVMRFNTEICGEAYSILATDVFPDLA 313

Query: 310 GNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSP 369
           G  +     + + + ++ LE   AD+G+ +TL   GI E+ L +L  D+++Q RLL  +P
Sbjct: 314 GTPA----AKRANQFIDRLEALSADLGLEQTLREVGIGEADLATLASDSMKQTRLLVNNP 369

Query: 370 LPLLEADIRAIYEAAF 385
             + E D  AIY+AAF
Sbjct: 370 REVSETDALAIYKAAF 385


Lambda     K      H
   0.318    0.135    0.381 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 363
Number of extensions: 21
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 395
Length of database: 385
Length adjustment: 31
Effective length of query: 364
Effective length of database: 354
Effective search space:   128856
Effective search space used:   128856
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory